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Mesarich CH, Barnes I, Bradley EL, de la Rosa S, de Wit PJGM, Guo Y, Griffiths SA, Hamelin RC, Joosten MHAJ, Lu M, McCarthy HM, Schol CR, Stergiopoulos I, Tarallo M, Zaccaron AZ, Bradshaw RE. Beyond the genomes of Fulvia fulva (syn. Cladosporium fulvum) and Dothistroma septosporum: New insights into how these fungal pathogens interact with their host plants. MOLECULAR PLANT PATHOLOGY 2023; 24:474-494. [PMID: 36790136 PMCID: PMC10098069 DOI: 10.1111/mpp.13309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F. fulva is a pathogen of tomato, whilst D. septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F. fulva and D. septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F. fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D. septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F. fulva and D. septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F. fulva and D. septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D. septosporum population. In this review, we specifically summarize advances made in our understanding of the F. fulva-tomato and D. septosporum-pine pathosystems over the last 10 years.
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Affiliation(s)
- Carl H Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Ellie L Bradley
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
| | - Yanan Guo
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | | | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, Québec, Canada
| | | | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hannah M McCarthy
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Christiaan R Schol
- Laboratory of Phytopathology, Wageningen University, Wageningen, Netherlands
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Ioannis Stergiopoulos
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | - Mariana Tarallo
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Alex Z Zaccaron
- Department of Plant Pathology, University of California Davis, Davis, California, USA
| | - Rosie E Bradshaw
- Bioprotection Aotearoa, Massey University, Palmerston North, New Zealand
- Laboratory of Molecular Plant Pathology, School of Natural Sciences, Massey University, Palmerston North, New Zealand
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van der Nest A, Wingfield MJ, Sadiković D, Mullett MS, Marçais B, Queloz V, Adamčíková K, Davydenko K, Barnes I. Population structure and diversity of the needle pathogen Dothistroma pini suggests human-mediated movement in Europe. Front Genet 2023; 14:1103331. [PMID: 36873952 PMCID: PMC9978111 DOI: 10.3389/fgene.2023.1103331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/27/2023] [Indexed: 02/18/2023] Open
Abstract
Dothistroma needle blight (DNB) is an important disease of Pinus species that can be caused by one of two distinct but closely related pathogens; Dothistroma septosporum and Dothistroma pini. Dothistroma septosporum has a wide geographic distribution and is relatively well-known. In contrast, D. pini is known only from the United States and Europe, and there is a distinct lack of knowledge regarding its population structure and genetic diversity. The recent development of 16 microsatellite markers for D. pini provided an opportunity to investigate the diversity, structure, and mode of reproduction for populations collected over a period of 12 years, on eight different hosts in Europe. In total, 345 isolates from Belgium, the Czech Republic, France, Hungary, Romania, Western Russia, Serbia, Slovakia, Slovenia, Spain, Switzerland, and Ukraine were screened using microsatellite and species-specific mating type markers. A total of 109 unique multilocus haplotypes were identified and structure analyses suggested that the populations are influenced by location rather than host species. Populations from France and Spain displayed the highest levels of genetic diversity followed by the population in Ukraine. Both mating types were detected in most countries, with the exception of Hungary, Russia and Slovenia. Evidence for sexual recombination was supported only in the population from Spain. The observed population structure and several shared haplotypes between non-bordering countries provides good evidence that the movement of D. pini in Europe has been strongly influenced by human activity in Europe.
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Affiliation(s)
- Ariska van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Dušan Sadiković
- Slovenian Forestry Institute, Ljubljana, Slovenia.,Southern Swedish Forest Research Centre, Swedish University of Agricultural Science, Alnarp, Sweden
| | - Martin S Mullett
- Phytophthora Research Centre, Mendel University in Brno, Brno, Czechia
| | - Benoit Marçais
- Université de Lorraine, INRAE-Grand-Est, UMR1136 Interactions Arbres, Microorganismes, Nancy, France
| | - Valentin Queloz
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Katarina Adamčíková
- Institute of Forest Ecology Slovak Academy of Sciences, Department of Plant Pathology and Mycology, Nitra, Slovakia
| | - Kateryna Davydenko
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Science, Uppsala, Sweden.,Ukrainian Forest Research Institute, Forestry and Forest Melioration, Kharkiv, Ukraine, Slovakia
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Radoslava J, Katarína A. Development and changes in pathogens population causing Dothistroma needle blight in Pinus nigra plantation in Strážovské vrchy Mts. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01135-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Aylward J, Havenga M, Wingfield BD, Wingfield MJ, Dreyer LL, Roets F, Steenkamp ET. Novel mating-type-associated genes and gene fragments in the genomes of Mycosphaerellaceae and Teratosphaeriaceae fungi. Mol Phylogenet Evol 2022; 171:107456. [DOI: 10.1016/j.ympev.2022.107456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 11/27/2022]
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Oskay F, Lehtijärvi A, Lehtijärvi HTD. Detection and Identification of the Causal Agents of Dothistroma Needle Blight. Methods Mol Biol 2022; 2536:155-166. [PMID: 35819604 DOI: 10.1007/978-1-0716-2517-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dothistroma needle blight (DNB) is one of the most damaging foliage diseases of pine in plantations and natural forests worldwide and is caused by two closely related fungi: Dothistroma septosporum and D. pini, which are virtually impossible to differentiate from each other based on morphology. Although diagnosis of DNB based on symptoms is relatively reliable in the later stages of the disease when fruit bodies (conidiomata) are formed, for diagnosis in the early stages, as well as identification of the causal agent at species level, molecular methods are required. In addition, reliable and sensitive diagnostics before sporulation is a prerequisite for early detection to minimize accidental introductions of disease through movement of infected plant materials, especially seedlings. While amplification and sequencing of the ITS region of the rDNA alone is not reliable to differentiate the two species, conventional PCR (cPCR) using species-specific primers or mating type-specific primers and quantitative PCR (qPCR) are widely used and accepted molecular methods to identify and differentiate the DNB pathogens, either from cultures or directly from needles.
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Affiliation(s)
- Funda Oskay
- Faculty of Forestry, Çankırı Karatekin University, Çankırı, Turkey.
| | - Asko Lehtijärvi
- Isparta University of Applied Sciences, Sütçüler Prof. Dr. Hasan Gürbüz Vocational School, Isparta, Turkey
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Zhao P, Crous P, Hou L, Duan W, Cai L, Ma Z, Liu F. Fungi of quarantine concern for China I: Dothideomycetes. PERSOONIA 2021; 47:45-105. [PMID: 37693796 PMCID: PMC10486631 DOI: 10.3767/persoonia.2021.47.02] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/09/2021] [Indexed: 11/25/2022]
Abstract
The current list of Chinese quarantine pests includes 130 fungal species. However, recent changes in the taxonomy of fungi following the one fungus = one name initiative and the implementation of DNA phylogeny in taxonomic revisions, resulted in many changes of these species names, necessitating an update of the current list. In addition, many quarantine fungi lack modern morphological descriptions and authentic DNA sequences, posing significant challenges for the development of diagnostic protocols. The aim of the present study was to review the taxonomy and names of the 33 Chinese quarantine fungi in Dothideomycetes, and provide reliable DNA barcodes to facilitate rapid identification. Of these, 23 names were updated according to the single name nomenclature system, including one new combination, namely Cophinforma tumefaciens comb. nov. (syn. Sphaeropsis tumefaciens). On the basis of phylogenetic analyses and morphological comparisons, a new genus Xenosphaeropsis is introduced to accommodate the monotypic species Xenosphaeropsis pyriputrescens comb. nov. (syn. Sphaeropsis pyriputrescens), the causal agent of a post-harvest disease of pears. Furthermore, four lectotypes (Ascochyta petroselini, Mycosphaerella ligulicola, Physalospora laricina, Sphaeria lingam), three epitypes (Ascochyta petroselini, Phoma lycopersici, Sphaeria lingam), and two neotypes (Ascochyta pinodella, Deuterophoma tracheiphila) are designated to stabilise the use of these names. A further four reference strains are introduced for Cophinforma tumefaciens, Helminthosporium solani, Mycocentrospora acerina, and Septoria linicola. In addition, to assist future studies on these important pathogens, we sequenced and assembled whole genomes for 17 species, including Alternaria triticina, Boeremia foveata, B. lycopersici, Cladosporium cucumerinum, Didymella glomerata, Didymella pinodella, Diplodia mutila, Helminthosporium solani, Mycocentrospora acerina, Neofusicoccum laricinum, Parastagonospora pseudonodorum, Plenodomus libanotidis, Plenodomus lingam, Plenodomus tracheiphilus, Septoria petroselini, Stagonosporopsis chrysanthemi, and Xenosphaeropsis pyriputrescens. Citation: Zhao P, Crous PW, Hou LW, et al. 2021. Fungi of quarantine concern for China I: Dothideomycetes. Persoonia 47: 45-105. https://doi.org/10.3767/persoonia.2021.47.02.
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Affiliation(s)
- P. Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - L.W. Hou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - W.J. Duan
- Ningbo Academy of Inspection and Quarantine, Ningbo 315012, China
- Ningbo Customs District P. R. China, Ningbo 315012, China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Z.Y. Ma
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - F. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Rapid Detection of Pine Pathogens Lecanosticta acicola, Dothistroma pini and D. septosporum on Needles by Probe-Based LAMP Assays. FORESTS 2021. [DOI: 10.3390/f12040479] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Needle blights are serious needle fungal diseases affecting pines both in natural and productive forests. Among needle blight agents, the ascomycetes Lecanosticta acicola, Dothistroma pini and D. septosporum are of particular concern. These pathogens need specific, fast and accurate diagnostics since they are regulated species in many countries and may require differential management measures. Due to the similarities in fungal morphology and the symptoms they elicit, these species are hard to distinguish using morphological characteristics. The symptoms can also be confused with those caused by insects or abiotic agents. DNA-based detection is therefore recommended. However, the specific PCR assays that have been produced to date for the differential diagnosis of these pathogens can be applied only in a well-furnished laboratory and the procedure takes a relatively long execution time. Surveillance and forest protection would benefit from a faster diagnostic method, such as a loop-mediated isothermal amplification (LAMP) assay, which requires less sophisticated equipment and can also be deployed directly on-site using portable devices. LAMP assays for the rapid and early detection of L. acicola, D. pini and D. septosporum were developed in this work. Species-specific LAMP primers and fluorescent assimilating probes were designed for each assay, targeting the beta tubulin (β-tub2) gene for the two Dothistroma species and the elongation factor (EF-1α) region for L. acicola. Each reaction detected its respective pathogen rapidly and with high specificity and sensitivity in DNA extracts from both pure fungal cultures and directly from infected pine needles. These qualities and the compatibility with inexpensive portable instrumentation position these LAMP assays as an effective method for routine phytosanitary control of plant material in real time, and they could profitably assist the management of L. acicola, D. pini and D. septosporum.
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Worldwide Genetic Structure Elucidates the Eurasian Origin and Invasion Pathways of Dothistroma septosporum, Causal Agent of Dothistroma Needle Blight. J Fungi (Basel) 2021; 7:jof7020111. [PMID: 33546260 PMCID: PMC7913368 DOI: 10.3390/jof7020111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022] Open
Abstract
Dothistroma septosporum, the primary causal agent of Dothistroma needle blight, is one of the most significant foliar pathogens of pine worldwide. Its wide host and environmental ranges have led to its global success as a pathogen and severe economic damage to pine forests in many regions. This comprehensive global population study elucidated the historical migration pathways of the pathogen to reveal the Eurasian origin of the fungus. When over 3800 isolates were examined, three major population clusters were revealed: North America, Western Europe, and Eastern Europe, with distinct subclusters in the highly diverse Eastern European cluster. Modeling of historical scenarios using approximate Bayesian computation revealed the North American cluster was derived from an ancestral population in Eurasia. The Northeastern European subcluster was shown to be ancestral to all other European clusters and subclusters. The Turkish subcluster diverged first, followed by the Central European subcluster, then the Western European cluster, which has subsequently spread to much of the Southern Hemisphere. All clusters and subclusters contained both mating-types of the fungus, indicating the potential for sexual reproduction, although asexual reproduction remained the primary mode of reproduction. The study strongly suggests the native range of D. septosporum to be in Eastern Europe (i.e., the Baltic and Western Russia) and Western Asia.
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Capron A, Feau N, Heinzelmann R, Barnes I, Benowicz A, Bradshaw RE, Dale A, Lewis KJ, Owen TJ, Reich R, Ramsfield TD, Woods AJ, Hamelin RC. Signatures of Post-Glacial Genetic Isolation and Human-Driven Migration in the Dothistroma Needle Blight Pathogen in Western Canada. PHYTOPATHOLOGY 2021; 111:116-127. [PMID: 33112215 DOI: 10.1094/phyto-08-20-0350-fi] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Many current tree improvement programs are incorporating assisted gene flow strategies to match reforestation efforts with future climates. This is the case for the lodgepole pine (Pinus contorta var. latifolia), the most extensively planted tree in western Canada. Knowledge of the structure and origin of pathogen populations associated with this tree would help improve the breeding effort. Recent outbreaks of the Dothistroma needle blight (DNB) pathogen Dothistroma septosporum on lodgepole pine in British Columbia and its discovery in Alberta plantations raised questions about the diversity and population structure of this pathogen in western Canada. Using genotyping-by-sequencing on 119 D. septosporum isolates from 16 natural pine populations and plantations from this area, we identified four genetic lineages, all distinct from the other DNB lineages from outside of North America. Modeling of the population history indicated that these lineages diverged between 31.4 and 7.2 thousand years ago, coinciding with the last glacial maximum and the postglacial recolonization of lodgepole pine in western North America. The lineage found in the Kispiox Valley from British Columbia, where an unprecedented DNB epidemic occurred in the 1990s, was close to demographic equilibrium and displayed a high level of haplotypic diversity. Two lineages found in Alberta and Prince George (British Columbia) showed departure from random mating and contemporary gene flow, likely resulting from pine breeding activities and material exchanges in these areas. The increased movement of planting material could have some major consequences by facilitating secondary contact between genetically isolated DNB lineages, possibly resulting in new epidemics.
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Affiliation(s)
- Arnaud Capron
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Renate Heinzelmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Andy Benowicz
- Alberta Agriculture and Forestry, 9920-108 Street, Edmonton, AB, T5K 2M4, Canada
| | - Rosie E Bradshaw
- School of Fundamental Sciences, Massey University, Palmerston North, 4410, New Zealand
| | - Angela Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- SC-New Construction Materials, FPInnovations, Vancouver, BC, V6T 1Z4, Canada
| | - Kathy J Lewis
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, V2N 4Z9, Canada
| | - Timothy J Owen
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, V2N 4Z9, Canada
| | - Richard Reich
- Natural Resources and Forest Technology, College of New Caledonia, Prince George, BC, V2N 1P8, Canada
| | - Tod D Ramsfield
- Natural Resources Canada, Canadian Forest Service, 5320 - 122 St., Edmonton, AB, T6H 3S5, Canada
| | - Alex J Woods
- BC Ministry of Forests Lands and Natural Resource Operations and Rural Development, Skeena Region, Smithers, BC, V0J 2N0, Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Faculté de foresterie et géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V0A6, Canada
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Havenga M, Wingfield BD, Wingfield MJ, Roets F, Dreyer LL, Tatham CT, Duong TA, Wilken PM, Chen S, Aylward J. Mating strategy and mating type distribution in six global populations of the Eucalyptus foliar pathogen Teratosphaeria destructans. Fungal Genet Biol 2020; 137:103350. [DOI: 10.1016/j.fgb.2020.103350] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/21/2020] [Accepted: 01/29/2020] [Indexed: 12/18/2022]
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Du XH, Wu D, Kang H, Wang H, Xu N, Li T, Chen K. Heterothallism and potential hybridization events inferred for twenty-two yellow morel species. IMA Fungus 2020; 11:4. [PMID: 32617256 PMCID: PMC7325075 DOI: 10.1186/s43008-020-0027-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 01/06/2020] [Indexed: 01/22/2023] Open
Abstract
Mating-type genes are central to sexual reproduction in ascomycete fungi and result in the establishment of reproductive barriers. Together with hybridization, they both play important roles in the evolution of fungi. Recently, potential hybridization events and MAT genes were separately found in the Elata Clade of Morchella. Herein, we characterized the MAT1-1-1 and MAT1-2-1 genes of twenty-two species in the Esculenta Clade, another main group in the genus Morchella, and proved heterothallism to be the predominant mating strategy among the twenty-two species tested. Ascospores of these species were multi-nuclear and had many mitochondrial nucleoids. The number of ascospore nuclei might be positively related with the species distribution range. Phylogenetic analyses of MAT1-1-1, MAT1-2-1, intergenic spacer (IGS), and partial histone acetyltransferase ELP3 (F1) were performed and compared with the species phylogeny framework derived from the ribosomal internal transcribed spacer region (ITS) and translation elongation factor 1-alpha (EF1-a) to evaluate their species delimitation ability and investigate potential hybridization events. Conflicting topologies among these genes genealogies and the species phylogeny were revealed and hybridization events were detected between several species. Different evolutionary patterns were suggested for MAT genes between the Esculenta and the Elata Clades. Complex evolutionary trajectories of MAT1-1-1, MAT1-2-1, F1 and IGS in the Esculenta Clade were highlighted. These findings contribute to a better understanding of the importance of hybridization and gene transfer in Morchella and especially for the appearance of reproductive modes during its evolutionary process.
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Affiliation(s)
- Xi-Hui Du
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331 China
| | - Dongmei Wu
- Biotechnology Research Institute, Xinjiang Academy Agricultural Reclamation of Sciences, Shihezi, 832000 China
| | - Heng Kang
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Hanchen Wang
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331 China
| | - Nan Xu
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331 China
| | - Tingting Li
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331 China
| | - Keliang Chen
- College of Life Sciences, Chongqing Normal University, Chongqing, 401331 China
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Reduced Virulence of an Introduced Forest Pathogen over 50 Years. Microorganisms 2019; 7:microorganisms7100420. [PMID: 31590374 PMCID: PMC6843257 DOI: 10.3390/microorganisms7100420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/21/2022] Open
Abstract
Pathogen incursions are a major impediment for global forest health. How pathogens and forest trees coexist over time, without pathogens simply killing their long-lived hosts, is a critical but unanswered question. The Dothistroma Needle Blight pathogen Dothistroma septosporum was introduced into New Zealand in the 1960s and remains a low-diversity, asexual population, providing a unique opportunity to analyze the evolution of a forest pathogen. Isolates of D. septosporum collected from commercial pine forests over 50 years were compared at whole-genome and phenotype levels. Limited genome diversity and increased diversification among recent isolates support the premise of a single introduction event. Isolates from the 1960s show significantly elevated virulence against Pinus radiata seedlings and produce higher levels of the virulence factor dothistromin compared to isolates collected in the 1990s and 2000s. However, later isolates have no increased tolerance to copper, used in fungicide treatments of infested forests and traditionally assumed to be a strong selection pressure. The isolated New Zealand population of this forest pathogen therefore appears to have become less virulent over time, likely in part to maintain the viability of its long-lived host. This finding has broad implications for forest health and highlights the benefits of long-term pathogen surveys.
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Bradshaw RE, Sim AD, Chettri P, Dupont P, Guo Y, Hunziker L, McDougal RL, Van der Nest A, Fourie A, Wheeler D, Cox MP, Barnes I. Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin-producing strains. MOLECULAR PLANT PATHOLOGY 2019; 20:784-799. [PMID: 30938073 PMCID: PMC6637865 DOI: 10.1111/mpp.12791] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Dothistroma needle blight is one of the most devastating pine tree diseases worldwide. New and emerging epidemics have been frequent over the last 25 years, particularly in the Northern Hemisphere, where they are in part associated with changing weather patterns. One of the main Dothistroma needle blight pathogens, Dothistroma septosporum, has a global distribution but most molecular plant pathology research has been confined to Southern Hemisphere populations that have limited genetic diversity. Extensive genomic and transcriptomic data are available for a D. septosporum reference strain from New Zealand, where an introduced clonal population of the pathogen predominates. Due to the global importance of this pathogen, we determined whether the genome of this reference strain is representative of the species worldwide by sequencing the genomes of 18 strains sampled globally from different pine hosts. Genomic polymorphism shows substantial variation within the species, clustered into two distinct groups of strains with centres of diversity in Central and South America. A reciprocal chromosome translocation uniquely identifies the New Zealand strains. Globally, strains differ in their production of the virulence factor dothistromin, with extremely high production levels in strain ALP3 from Germany. Comparisons with the New Zealand reference revealed that several strains are aneuploids; for example, ALP3 has duplications of three chromosomes. Increased gene copy numbers therefore appear to contribute to increased production of dothistromin, emphasizing that studies of population structure are a necessary adjunct to functional analyses of genetic polymorphisms to identify the molecular basis of virulence in this important forest pathogen.
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Affiliation(s)
- Rosie E. Bradshaw
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Andre D. Sim
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Pranav Chettri
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Pierre‐Yves Dupont
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
- Institute of Environmental Science and ResearchChristchurch8041New Zealand
| | - Yanan Guo
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Lukas Hunziker
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | | | - Ariska Van der Nest
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - Arista Fourie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
| | - David Wheeler
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
- NSW Department of Primary IndustriesOrange Agricultural InstituteAustralia
| | - Murray P. Cox
- School of Fundamental Sciences and Bio‐Protection Research CentreMassey UniversityPalmerston North4410New Zealand
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI)University of PretoriaPretoriaSouth Africa
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15
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Pearce TL, Scott JB, Pilkington SJ, Pethybridge SJ, Hay FS. Evidence for Sexual Recombination in Didymella tanaceti Populations, and Their Evolution Over Spring Production in Australian Pyrethrum Fields. PHYTOPATHOLOGY 2019; 109:155-168. [PMID: 29989847 DOI: 10.1094/phyto-08-17-0280-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tan spot, caused by Didymella tanaceti, is one of the most important foliar diseases affecting pyrethrum in Tasmania, Australia. Population dynamics, including mating-type ratios and genetic diversity of D. tanaceti, was characterized within four geographically separated fields in both late winter and spring 2012. A set of 10 microsatellite markers was developed and used to genotype 774 D. tanaceti isolates. Isolates were genotypically diverse, with 123 multilocus genotypes (MLG) identified across the four fields. Fifty-eight MLG contained single isolates and Psex analysis estimated that, within many of the recurrent MLG, there were multiple clonal lineages derived from recombination. Isolates of both mating types were at a 1:1 ratio following clone correction in each field at each sampling period, which was suggestive of sexual recombination. No evidence of genetic divergence of isolates of each mating type was identified, indicating admixture within the population. Linkage equilibrium in two of the four field populations sampled in late winter could not be discounted following clone correction. Evaluation of temporal changes in gene and genotypic diversity identified that they were both similar for the two sampling periods despite an increased D. tanaceti isolation frequency in spring. Genetic differentiation was similar in populations sampled between the two sampling periods within fields or between fields. These results indicated that sexual reproduction may have contributed to tan spot epidemics within Australian pyrethrum fields and has contributed to a genetically diverse D. tanaceti population.
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Affiliation(s)
- Tamieka L Pearce
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Jason B Scott
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Stacey J Pilkington
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Sarah J Pethybridge
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Frank S Hay
- First, second, and third authors, Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania 7320, Australia; fourth and fifth authors, Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
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16
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Piotrowska MJ, Riddell C, Hoebe PN, Ennos RA. Planting exotic relatives has increased the threat posed by Dothistroma septosporum to the Caledonian pine populations of Scotland. Evol Appl 2018; 11:350-363. [PMID: 29632553 PMCID: PMC5881121 DOI: 10.1111/eva.12562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/08/2017] [Indexed: 12/27/2022] Open
Abstract
To manage emerging forest diseases and prevent their occurrence in the future, it is essential to determine the origin(s) of the pathogens involved and identify the management practices that have ultimately caused disease problems. One such practice is the widespread planting of exotic tree species within the range of related native taxa. This can lead to emerging forest disease both by facilitating introduction of exotic pathogens and by providing susceptible hosts on which epidemics of native pathogens can develop. We used microsatellite markers to determine the origins of the pathogen Dothistroma septosporum responsible for the current outbreak of Dothistroma needle blight (DNB) on native Caledonian Scots pine (Pinus sylvestris) populations in Scotland and evaluated the role played by widespread planting of two exotic pine species in the development of the disease outbreak. We distinguished three races of D. septosporum in Scotland, one of low genetic diversity associated with introduced lodgepole pine (Pinus contorta), one of high diversity probably derived from the DNB epidemic on introduced Corsican pine (Pinus nigra subsp. laricio) in England and a third of intermediate diversity apparently endemic on Caledonian Scots pine. These races differed for both growth rate and exudate production in culture. Planting of exotic pine stands in the UK appears to have facilitated the introduction of two exotic races of D. septosporum into Scotland which now pose a threat to native Caledonian pines both directly and through potential hybridization and introgression with the endemic race. Our results indicate that both removal of exotic species from the vicinity of Caledonian pine populations and restriction of movement of planting material are required to minimize the impact of the current DNB outbreak. They also demonstrate that planting exotic species that are related to native species reduces rather than enhances the resilience of forests to pathogens.
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Affiliation(s)
- Marta J. Piotrowska
- Crop and Soil Systems Research GroupScotland's Rural CollegeEdinburghUK
- The Institute of Biological Chemistry, Biophysics and BioengineeringHeriot‐Watt UniversityEdinburghUK
| | - Carolyn Riddell
- Institute of Evolutionary BiologyAshworth LaboratoriesUniversity of EdinburghEdinburghUK
- Forest ResearchNorthern Research StationRoslinUK
| | - Peter N. Hoebe
- Crop and Soil Systems Research GroupScotland's Rural CollegeEdinburghUK
| | - Richard A. Ennos
- Institute of Evolutionary BiologyAshworth LaboratoriesUniversity of EdinburghEdinburghUK
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17
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Adamson K, Mullett MS, Solheim H, Barnes I, Müller MM, Hantula J, Vuorinen M, Kačergius A, Markovskaja S, Musolin DL, Davydenko K, Keča N, Ligi K, Priedite RD, Millberg H, Drenkhan R. Looking for relationships between the populations of Dothistroma septosporum in northern Europe and Asia. Fungal Genet Biol 2017; 110:15-25. [PMID: 29223582 DOI: 10.1016/j.fgb.2017.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 11/06/2017] [Accepted: 12/05/2017] [Indexed: 01/29/2023]
Abstract
Dothistroma septosporum, a notorious pine needle pathogen with an unknown historical geographic origin and poorly known distribution pathways, is nowadays found almost in all areas inhabited by pines (Pinus spp.). The main aim of this study was to determine the relationship between North European and East Asian populations. In total, 238 Eurasian D. septosporum isolates from 11 countries, including 211 isolates from northern Europe, 16 isolates from Russian Far East and 11 isolates from Bhutan were analysed using 11 species-specific microsatellite and mating type markers. The most diverse populations were found in northern Europe, including the Baltic countries, Finland and European Russia. Notably, D. septosporum has not caused heavy damage to P. sylvestris in northern Europe, which may suggest a long co-existence of the host and the pathogen. No indication was obtained that the Russian Far East or Bhutan could be the indigenous area of D. septosporum, as the genetic diversity of the fungus there was low and evidence suggests gene flow from northern Europe to Russian Far East. On the western coast of Norway, a unique genetic pattern was observed, which differed from haplotypes dominating other Fennoscandian populations. As an agent of dothistroma needle blight, only D. septosporum was documented in northern Europe and Asia, while D. pini was found in Ukraine and Serbia.
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Affiliation(s)
- Kalev Adamson
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia.
| | | | | | - Irene Barnes
- Department of Genetics, FABI, University of Pretoria, Pretoria, South Africa
| | | | - Jarkko Hantula
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Martti Vuorinen
- Natural Resources Institute Finland (Luke), Suonenjoki, Finland
| | - Audrius Kačergius
- Vokė Branch of Lithuanian Research Centre for Agriculture and Forestry, Vilnius, Lithuania
| | | | - Dmitry L Musolin
- Saint Petersburg State Forest Technical University, Saint Petersburg, Russia
| | - Kateryna Davydenko
- Department of Biotechnology and Environment, Kharkiv Zooveterinary Academy, Kharkiv, Ukraine; Department Forest Mycology and Plant Pathology, Swedish Universiy of Agriculture Science, Uppsala, Sweden
| | - Nenad Keča
- Faculty of Forestry-University of Belgrade, Belgrade, Serbia
| | - Karli Ligi
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | | | - Hanna Millberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rein Drenkhan
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, Tartu, Estonia
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18
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Videira S, Groenewald J, Nakashima C, Braun U, Barreto R, de Wit P, Crous P. Mycosphaerellaceae - Chaos or clarity? Stud Mycol 2017; 87:257-421. [PMID: 29180830 PMCID: PMC5693839 DOI: 10.1016/j.simyco.2017.09.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The Mycosphaerellaceae represent thousands of fungal species that are associated with diseases on a wide range of plant hosts. Understanding and stabilising the taxonomy of genera and species of Mycosphaerellaceae is therefore of the utmost importance given their impact on agriculture, horticulture and forestry. Based on previous molecular studies, several phylogenetic and morphologically distinct genera within the Mycosphaerellaceae have been delimited. In this study a multigene phylogenetic analysis (LSU, ITS and rpb2) was performed based on 415 isolates representing 297 taxa and incorporating ex-type strains where available. The main aim of this study was to resolve the phylogenetic relationships among the genera currently recognised within the family, and to clarify the position of the cercosporoid fungi among them. Based on these results many well-known genera are shown to be paraphyletic, with several synapomorphic characters that have evolved more than once within the family. As a consequence, several old generic names including Cercosporidium, Fulvia, Mycovellosiella, Phaeoramularia and Raghnildiana are resurrected, and 32 additional genera are described as new. Based on phylogenetic data 120 genera are now accepted within the family, but many currently accepted cercosporoid genera still remain unresolved pending fresh collections and DNA data. The present study provides a phylogenetic framework for future taxonomic work within the Mycosphaerellaceae.
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Key Words
- Adelopus gaeumannii T. Rohde
- Amycosphaerella keniensis (Crous & T.A. Cout.) Videira & Crous
- Australosphaerella Videira & Crous
- Australosphaerella nootherensis (Carnegie) Videira & Crous
- Biharia vangueriae Thirum. & Mishra
- Brunswickiella Videira & Crous
- Brunswickiella parsonsiae (Crous & Summerell) Videira & Crous
- Catenulocercospora C. Nakash., Videira & Crous
- Catenulocercospora fusimaculans (G.F. Atk.) C. Nakash., Videira & Crous
- Cercoramularia Videira, H.D. Shin, C. Nakash. & Crous
- Cercoramularia koreana Videira, H.D. Shin, C. Nakash. & Crous
- Cercospora brachycarpa Syd.
- Cercospora cajani Henn.
- Cercospora desmodii Ellis & Kellerm.
- Cercospora ferruginea Fuckel
- Cercospora gnaphaliacea Cooke
- Cercospora gomphrenicola Speg.
- Cercospora henningsii Allesch.
- Cercospora mangiferae Koord.
- Cercospora microsora Sacc.
- Cercospora rosicola Pass.
- Cercospora smilacis Thüm.
- Cercospora tiliae Peck
- Cercosporidium californicum (S.T. Koike & Crous) Videira & Crous
- Cercosporidium helleri Earle
- Chuppomyces Videira & Crous
- Chuppomyces handelii (Bubák) U. Braun, C. Nakash., Videira & Crous
- Cladosporium bacilligerum Mont. & Fr.
- Cladosporium chaetomium Cooke
- Cladosporium fulvum Cooke
- Cladosporium lonicericola Yong H. He & Z.Y. Zhang
- Cladosporium personatum Berk. & M.A. Curtis
- Clarohilum Videira & Crous
- Clarohilum henningsii (Allesch.) Videira & Crous
- Clasterosporium degenerans Syd. & P. Syd.
- Clypeosphaerella calotropidis (Ellis & Everh.) Videira & Crous
- Collarispora Videira & Crous
- Collarispora valgourgensis (Crous) Videira & Crous
- Coremiopassalora U. Braun, C. Nakash., Videira & Crous
- Coremiopassalora eucalypti (Crous & Alfenas) U. Braun, C. Nakash., Videira & Crous
- Coremiopassalora leptophlebae (Crous et al.) U. Braun, C. Nakash., Videira & Crous
- Coryneum vitiphyllum Speschnew
- Cryptosporium acicola Thüm.
- Deightonomyces Videira & Crous
- Deightonomyces daleae (Ellis & Kellerm.) Videira & Crous
- Devonomyces Videira & Crous
- Devonomyces endophyticus (Crous & H. Sm. Ter) Videira & Crous
- Distocercosporaster Videira, H.D. Shin, C. Nakash. & Crous
- Distocercosporaster dioscoreae (Ellis & G. Martin) Videira, H.D. Shin, C. Nakash. & Crous
- Distomycovellosiella U. Braun, C. Nakash., Videira & Crous
- Distomycovellosiella brachycarpa (Syd.) U. Braun, C. Nakash., Videira & Crous
- Exopassalora Videira & Crous
- Exopassalora zambiae (Crous & T.A. Cout.) Videira & Crous
- Exosporium livistonicola U. Braun, Videira & Crous for Distocercospora livistonae U. Braun & C.F. Hill
- Exutisphaerella Videira & Crous
- Exutisphaerella laricina (R. Hartig) Videira & Crous
- Fusoidiella anethi (Pers.) Videira & Crous
- Graminopassalora U. Braun, C. Nakash., Videira & Crous
- Graminopassalora graminis (Fuckel) U. Braun, C. Nakash., Videira & Crous
- Helicoma fasciculatum Berk. & M.A. Curtis.
- Hyalocercosporidium Videira & Crous
- Hyalocercosporidium desmodii Videira & Crous
- Hyalozasmidium U. Braun, C. Nakash., Videira & Crous
- Hyalozasmidium aerohyalinosporum (Crous & Summerell) Videira & Crous
- Hyalozasmidium sideroxyli U. Braun, C. Nakash., Videira & Crous
- Isariopsis griseola Sacc.
- Madagascaromyces U. Braun, C. Nakash., Videira & Crous
- Madagascaromyces intermedius (Crous & M.J. Wingf.) Videira & Crous
- Micronematomyces U. Braun, C. Nakash., Videira & Crous
- Micronematomyces caribensis (Crous & Den Breeÿen) U. Braun, C. Nakash., Videira & Crous
- Micronematomyces chromolaenae (Crous & Den Breeÿen) U. Braun, C. Nakash., Videira & Crous
- Multi-gene phylogeny
- Mycosphaerella
- Neoceratosperma haldinae U. Braun, C. Nakash., Videira & Crous
- Neoceratosperma legnephoricola U. Braun, C. Nakash., Videira & Crous
- Neocercosporidium Videira & Crous
- Neocercosporidium smilacis (Thüm.) U. Braun, C. Nakash., Videira & Crous
- Neophloeospora Videira & Crous
- Neophloeospora maculans (Bérenger) Videira & Crous
- Nothopassalora U. Braun, C. Nakash., Videira & Crous
- Nothopassalora personata (Berk. & M.A. Curtis) U. Braun, C. Nakash., Videira & Crous
- Nothopericoniella Videira & Crous
- Nothopericoniella perseae-macranthae (Hosag. & U. Braun) Videira & Crous
- Nothophaeocryptopus Videira, C. Nakash., U. Braun, Crous
- Nothophaeocryptopus gaeumannii (T. Rohde) Videira, C. Nakash., U. Braun, Crous
- Pachyramichloridium Videira & Crous
- Pachyramichloridium pini (de Hoog & Rahman) U. Braun, C. Nakash., Videira & Crous
- Paracercosporidium Videira & Crous
- Paracercosporidium microsorum (Sacc.) U. Braun, C. Nakash., Videira & Crous
- Paracercosporidium tiliae (Peck) U. Braun, C. Nakash., Videira & Crous
- Paramycosphaerella wachendorfiae (Crous) Videira & Crous
- Paramycovellosiella Videira, H.D. Shin & Crous
- Paramycovellosiella passaloroides (G. Winter) Videira, H.D. Shin & Crous
- Parapallidocercospora Videira, Crous, U. Braun, C. Nakash.
- Parapallidocercospora colombiensis (Crous et al.) Videira & Crous
- Parapallidocercospora thailandica (Crous et al.) Videira & Crous
- Phaeocercospora juniperina (Georgescu & Badea) U. Braun, C. Nakash., Videira & Crous
- Plant pathogen
- Pleopassalora Videira & Crous
- Pleopassalora perplexa (Beilharz et al.) Videira & Crous
- Pleuropassalora U. Braun, C. Nakash., Videira & Crous
- Pleuropassalora armatae (Crous & A.R. Wood) U. Braun, C. Nakash., Videira & Crous
- Pluripassalora Videira & Crous
- Pluripassalora bougainvilleae (Munt.-Cvetk.) U. Braun, C. Nakash., Videira & Crous
- Pseudocercospora convoluta (Crous & Den Breeÿen) U. Braun, C. Nakash., Videira & Crous
- Pseudocercospora nodosa (Constant.) U. Braun, C. Nakash., Videira & Crous
- Pseudocercospora platanigena Videira & Crous for Stigmella platani Fuckel, non Pseudocercospora platani (J.M. Yen) J.M. Yen 1979
- Pseudocercospora zambiensis (Deighton) Crous & U. Braun
- Pseudopericoniella Videira & Crous
- Pseudopericoniella levispora (Arzanlou, W. Gams & Crous) Videira & Crous
- Pseudophaeophleospora U. Braun, C. Nakash., Videira & Crous
- Pseudophaeophleospora atkinsonii (Syd.) U. Braun, C. Nakash., Videira & Crous
- Pseudophaeophleospora stonei (Crous) U. Braun, C. Nakash., Videira & Crous
- Pseudozasmidium Videira & Crous
- Pseudozasmidium eucalypti (Crous & Summerell) Videira & Crous
- Pseudozasmidium nabiacense (Crous & Carnegie) Videira & Crous
- Pseudozasmidium parkii (Crous & Alfenas) Videira & Crous
- Pseudozasmidium vietnamense (Barber & T.I. Burgess) Videira & Crous
- Ragnhildiana ampelopsidis (Peck) U. Braun, C. Nakash., Videira & Crous
- Ragnhildiana diffusa (Heald & F.A. Wolf) Videira & Crous
- Ragnhildiana ferruginea (Fuckel) U. Braun, C. Nakash., Videira & Crous
- Ragnhildiana gnaphaliaceae (Cooke) Videira, H.D. Shin, C. Nakash. & Crous
- Ragnhildiana perfoliati (Ellis & Everh.) U. Braun, C. Nakash., Videira & Crous
- Ragnhildiana pseudotithoniae (Crous & Cheew.) U. Braun, C. Nakash., Videira & Crous
- Ramulispora sorghiphila U. Braun, C. Nakash., Videira & Crous
- Rhachisphaerella Videira & Crous
- Rhachisphaerella mozambica (Arzanlou & Crous) Videira & Crous
- Rosisphaerella Videira & Crous
- Rosisphaerella rosicola (Pass.) U. Braun, C. Nakash., Videira & Crous
- Scolicotrichum roumeguerei Briosi & Cavara
- Septoria martiniana Sacc
- Sphaerella araneosa Rehm
- Sphaerella laricina R. Hartig
- Stictosepta cupularis Petr.
- Stigmella platani Fuckel
- Sultanimyces Videira & Crous
- Sultanimyces vitiphyllus (Speschnew) Videira & Crous
- Tapeinosporium viride Bonord
- Taxonomy
- Utrechtiana roumeguerei (Cavara) Videira & Crous
- Virosphaerella Videira & Crous
- Virosphaerella irregularis (Cheew. et al.) Videira & Crous
- Virosphaerella pseudomarksii (Cheew. et al.) Videira & Crous
- Xenosonderhenioides Videira & Crous
- Xenosonderhenioides indonesiana C. Nakash., Videira & Crous
- Zasmidium arcuatum (Arzanlou et al.) Videira & Crous
- Zasmidium biverticillatum (Arzanlou & Crous) Videira & Crous
- Zasmidium cerophilum (Tubaki) U. Braun, C. Nakash., Videira & Crous
- Zasmidium daviesiae (Cooke & Massee) U. Braun, C. Nakash., Videira & Crous
- Zasmidium elaeocarpi U. Braun, C. Nakash., Videira & Crous
- Zasmidium eucalypticola U. Braun, C. Nakash., Videira & Crous
- Zasmidium grevilleae U. Braun, C. Nakash., Videira & Crous
- Zasmidium gupoyu (R. Kirschner) U. Braun, C. Nakash., Videira & Crous
- Zasmidium hakeae U. Braun, C. Nakash., Videira & Crous
- Zasmidium iteae (R. Kirschner) U. Braun, C. Nakash., Videira & Crous
- Zasmidium musae-banksii Videira & Crous for Ramichloridium australiense Arzanlou & Crous, non Zasmidium australiense (J.L. Mulder) U. Braun & Crous 2013
- Zasmidium musigenum Videira & Crous for Veronaea musae Stahel ex M.B. Ellis, non Zasmidium musae (Arzanlou & Crous) Crous & U. Braun 2010
- Zasmidium proteacearum (D.E. Shaw & Alcorn) U. Braun, C. Nakash. & Crous
- Zasmidium pseudotsugae (V.A.M. Mill. & Bonar) Videira & Crous
- Zasmidium pseudovespa (Carnegie) U. Braun, C. Nakash., Videira & Crous
- Zasmidium schini U. Braun, C. Nakash., Videira & Crous
- Zasmidium strelitziae (Arzanlou et al.) Videira & Crous
- Zasmidium tsugae (Dearn.) Videira & Crous
- Zasmidium velutinum (G. Winter) Videira & Crous
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Affiliation(s)
- S.I.R. Videira
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - J.Z. Groenewald
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - C. Nakashima
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie, 514-8507, Japan
| | - U. Braun
- Martin-Luther-Universität Halle-Wittenberg, Institut für Biologie, Bereich Geobotanik, Herbarium, Neuwerk 21, 06099, Halle (Saale), Germany
| | - R.W. Barreto
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - P.J.G.M. de Wit
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - P.W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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Bock CH, Hotchkiss MW, Young CA, Charlton ND, Chakradhar M, Stevenson KL, Wood BW. Population Genetic Structure of Venturia effusa, Cause of Pecan Scab, in the Southeastern United States. PHYTOPATHOLOGY 2017; 107:607-619. [PMID: 28414611 DOI: 10.1094/phyto-10-16-0376-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Venturia effusa is the most important pathogen of pecan in the southeastern United States. Little information exists on the population biology and genetic diversity of the pathogen. A hierarchical sampling of 784 isolates from 63 trees in 11 pecan orchards in the southeastern United States were screened against a set of 30 previously characterized microsatellite markers. Populations were collected from Georgia (n = 2), Florida (n = 1), Alabama (n = 2), Mississippi (n = 1), Louisiana (n = 1), Illinois (n = 1), Oklahoma (n = 1), Texas (n = 1), and Kansas (n = 1). Clonality was low in all orchard populations (≤10.1% of isolates), and there were consistently high levels of genotypic diversity (Shannon-Weiner's index = 3.49 to 4.59) and gene diversity (Nei's measure = 0.513 to 0.713). Analysis of molecular variance showed that, although 81% of genetic diversity occurred at the scale of the individual tree, 16% occurred between orchards and only 3% between trees within orchards. All populations could be differentiated from each other (P = 0.01), and various cluster analyses indicated that some populations were more closely related compared with other pairs of populations. This is indicative of some limited population differentiation in V. effusa in the southeastern United States. Bayesian and nearest-neighbor methods suggested eight clusters, with orchards from Georgia and Florida being grouped together. A minimum spanning tree of all 784 isolates also indicated some isolate identification with source population. Linkage disequilibrium was detected in all but one population (Kansas), although 8 of the 11 populations had <20% of loci at disequilibrium. A Mantel test demonstrated a relationship between physical and genetic distance between populations (Z = 11.9, r = 0.559, P = 0.001). None of the populations were at mutation-drift equilibrium. All but 3 of the 11 populations had a deficiency of gene diversity compared with that expected at mutation-drift equilibrium (indicating population expansion); the remaining populations had an excess of gene diversity compared with that expected at mutation-drift equilibrium (indicating a recent bottleneck). These observations are consistent with the known history of pecan and pecan scab, which is that V. effusa became an issue on cultivated pecan in the last approximately 120 years (recent population expansion). Recently reported mating type genes and the sexual stage of this fungus may help explain the observed population characteristics, which bear a strong resemblance to those of other well-characterized sexually reproducing ascomycete pathogens.
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Affiliation(s)
- Clive H Bock
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Michael W Hotchkiss
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Carolyn A Young
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Nikki D Charlton
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Mattupalli Chakradhar
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Katherine L Stevenson
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
| | - Bruce W Wood
- First, second, and seventh authors: United States Department of Agriculture-Agricultural Research Service Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA 31008; third, fourth, and fifth authors: The Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, OK 73401; sixth author: Department of Plant Pathology, Coastal Plain Experiment Station, University of Georgia, Tifton 31793
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Mullett M, Brown A, Fraser S, Baden R, Tubby K. Insights into the pathways of spread and potential origins of Dothistroma septosporum in Britain. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Crous PW, Groenewald JZ, Slippers B, Wingfield MJ. Global food and fibre security threatened by current inefficiencies in fungal identification. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160024. [PMID: 28080994 PMCID: PMC5095547 DOI: 10.1098/rstb.2016.0024] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2016] [Indexed: 01/02/2023] Open
Abstract
Fungal pathogens severely impact global food and fibre crop security. Fungal species that cause plant diseases have mostly been recognized based on their morphology. In general, morphological descriptions remain disconnected from crucially important knowledge such as mating types, host specificity, life cycle stages and population structures. The majority of current fungal species descriptions lack even the most basic genetic data that could address at least some of these issues. Such information is essential for accurate fungal identifications, to link critical metadata and to understand the real and potential impact of fungal pathogens on production and natural ecosystems. Because international trade in plant products and introduction of pathogens to new areas is likely to continue, the manner in which fungal pathogens are identified should urgently be reconsidered. The technologies that would provide appropriate information for biosecurity and quarantine already exist, yet the scientific community and the regulatory authorities are slow to embrace them. International agreements are urgently needed to enforce new guidelines for describing plant pathogenic fungi (including key DNA information), to ensure availability of relevant data and to modernize the phytosanitary systems that must deal with the risks relating to trade-associated plant pathogens.This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Pedro W Crous
- CBS-KNAW Fungal Biodiversity Centre, PO Box 85167, 3508 AD Utrecht, The Netherlands
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | - Bernard Slippers
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Michael J Wingfield
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
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Pearce TL, Scott JB, Hay FS, Pethybridge SJ. Mating-Type Gene Structure and Spatial Distribution of Didymella tanaceti in Pyrethrum Fields. PHYTOPATHOLOGY 2016; 106:1521-1529. [PMID: 27398744 DOI: 10.1094/phyto-01-16-0038-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Tan spot of pyrethrum (Tanacetum cinerariifolium) is caused by the ascomycete Didymella tanaceti. To assess the evolutionary role of ascospores in the assumed asexual species, the structure and arrangement of mating-type (MAT) genes were examined. A single MAT1-1 or MAT1-2 idiomorph was identified in all isolates examined, indicating that the species is heterothallic. The idiomorphs were flanked upstream and downstream by regions encoding pyridoxamine phosphate oxidase-like and DNA lyase-like proteins, respectively. A multiplex MAT-specific polymerase chain reaction assay was developed and used to genotype 325 isolates collected within two transects in each of four fields in Tasmania, Australia. The ratio of isolates of each mating-type in each transect was consistent with a 1:1 ratio. The spatial distribution of the isolates of the two mating-types within each transect was random for all except one transect for MAT1-1 isolates, indicating that clonal patterns of each mating-type were absent. However, evidence of a reduced selection pressure on MAT1-1 isolates was observed, with a second haplotype of the MAT1-1-1 gene identified in 4.4% of MAT1-1 isolates. In vitro crosses between isolates with opposite mating-types failed to produce ascospores. Although the sexual morph could not be induced, the occurrence of both mating-types in equal frequencies suggested that a cryptic sexual mode of reproduction may occur within field populations.
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Affiliation(s)
- Tamieka L Pearce
- First and second authors: Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia; and third and fourth authors: Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Jason B Scott
- First and second authors: Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia; and third and fourth authors: Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Frank S Hay
- First and second authors: Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia; and third and fourth authors: Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Sarah J Pethybridge
- First and second authors: Tasmanian Institute of Agriculture, School of Land and Food, University of Tasmania, Burnie, Tasmania 7320, Australia; and third and fourth authors: Cornell University, School of Integrative Plant Science, Section of Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
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Mating type genes in the genus Neofusicoccum: Mating strategies and usefulness in species delimitation. Fungal Biol 2016; 121:394-404. [PMID: 28317541 DOI: 10.1016/j.funbio.2016.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/25/2016] [Indexed: 12/16/2022]
Abstract
The genus Neofusicoccum includes species with wide geographical and plant host distribution, some of them of economic importance. The genus currently comprises 27 species that are difficult to identify based on morphological features alone. Thus, species differentiation is based on phylogenetic species recognition using multigene genealogies. In this study, we characterised the mating type genes of Neofusicoccum species. Specific primers were designed to amplify and sequence MAT genes in several species and a PCR-based mating type diagnostic assay was developed. Homothallism was the predominant mating strategy among the species tested. Furthermore, the potential of mating type gene sequences for species delimitation was evaluated. Phylogenetic analyses were performed on both MAT genes and compared with multigene genealogies using sequences of the ribosomal internal transcribed spacer region, translation elongation factor 1-alpha and beta-tubulin. Phylogenies based on mating type genes could discriminate between the species analysed and are in concordance with the results obtained with the more conventional multilocus phylogenetic analysis approach. Thus, MAT genes represent a powerful tool to delimit cryptic species in the genus Neofusicoccum.
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Mullett M, Peace A, Brown A. Persistence of Dothistroma septosporum on Abscised Pine Needles and its Implications for Disease Management. PLANT DISEASE 2016; 100:1271-1277. [PMID: 30686201 DOI: 10.1094/pdis-11-15-1306-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Dothistroma septosporum is a serious foliar pathogen of pines in Britain. To determine the contribution of spores produced on abscised needles to the D. septosporum inoculum load in a forest environment, survival of the fungus was investigated in commercially grown plantations of Corsican pine (Pinus nigra subsp. laricio) in southern England. The fungus persisted for longer in abscised needles retained in the canopy compared with needles on the litter layer of the forest floor. High relative humidity had a significant negative effect on persistence in the canopy needles, highlighting the effect of moisture on rates of microbial decay. The median lethal time 50 (LT50) of infective propagules from needles in the litter layer was 20 to 28 days, whereas for needles suspended in the canopy it was 34 to 48 days. Microsatellite markers revealed that the population of D. septosporum deemed persistent (i.e., recovered from abscised needles after exposure for 28 to 32 weeks) was similar to the general population of D. septosporum in the forest stand (i.e., isolates recovered from attached needles and after exposure for only 4 weeks). Overall, abscised needles with acervuli of D. septosporum contribute only moderately and for a limited time to inoculum levels of the pathogen in an infected forest stand.
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Affiliation(s)
- Martin Mullett
- Forest Research, Alice Holt Lodge, Farnham, Surrey, GU10 4LH, UK
| | - Andy Peace
- Forest Research, Northern Research Station, Roslin, Midlothian, EH25 9SY, UK
| | - Anna Brown
- Forestry Commission, Silvan House, 231 Corstorphine Road, Edinburgh, EH12 7AT, UK
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26
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The rise of Ramularia from the Mycosphaerella labyrinth. Fungal Biol 2015; 119:823-43. [PMID: 26321731 DOI: 10.1016/j.funbio.2015.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/23/2015] [Accepted: 06/08/2015] [Indexed: 11/20/2022]
Abstract
In this study we aimed to resolve the Ramularia endophylla species-complex by applying a polyphasic approach involving morphology and multi-gene phylogeny. Eleven partial genes were targeted for amplification and sequencing for a total of 81 isolates representing R. endophylla s. lat. and 32 isolates representing 11 Ramularia species that were previously linked to a Mycosphaerella sexual morph in literature. A Bayesian phylogenetic analysis, as well as a parsimony analysis, was performed on a combined five-locus dataset and the resulting trees showed significant support for three species within the complex, including the previously described R. endophylla and R. vizellae, and one novel species, Ramularia unterseheri. A parsimony analysis was also separately performed with mating-type gene sequences (MAT1-1-1 and MAT1-2-1) and the resulting tree topologies were in accordance with that of the multigene analysis. A bibliographic review of the proposed links between Ramularia spp. and their purported Mycosphaerella sexual morphs is also presented, confirming six connections in Ramularia. In spite of more than 10 000 species having been described in Mycosphaerella, the majority is shown to belong to other genera, suggesting that the taxa identified as Mycosphaerella in much of the plant pathology literature needs to be revisited.
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27
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Crous PW, Hawksworth DL, Wingfield MJ. Identifying and naming plant-pathogenic fungi: past, present, and future. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:247-267. [PMID: 26047568 DOI: 10.1146/annurev-phyto-080614-120245] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk. Our understanding of fungal biodiversity and fungal systematics has undergone an exponential leap, incorporating genomics, web-based systems, and DNA data for rapid identification to link species to metadata. The impact of our ability to recognize hitherto unknown organisms on plant pathology and trade is enormous and continues to grow. Major challenges for phytomycology are intertwined with the Genera of Fungi project, which adds DNA barcodes to known biodiversity and corrects the application of old, established names via epi- or neotypification. Implementing the one fungus-one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication of names of plant pathogens will rest.
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Affiliation(s)
- Pedro W Crous
- CBS-KNAW Fungal Biodiversity Centre, 3584 CT Utrecht, Netherlands;
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Boateng K, Lewis KJ. Spore Dispersal by Dothistroma septosporum in Northwest British Columbia. PHYTOPATHOLOGY 2015; 105:69-79. [PMID: 25014680 DOI: 10.1094/phyto-06-13-0175-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We studied spore dispersal by Dothistroma septosporum, causal agent of a serious outbreak of red band needle blight in lodgepole pine plantations in northwest British Columbia. Spore abundance was assessed at different distances and heights from inoculum sources and microclimatic factors were recorded during two consecutive years. Conidia were observed on spore traps from June to September during periods of rainfall. It was rare to detect spores more than 2 m away from inoculum sources. The timing and number of conidia dispersed were strongly tied to the climatic variables, particularly rainfall and leaf wetness. Should the trend toward increased spring and summer precipitation in the study area continue, the results suggest that disease spread and intensification will also increase. Increasing the planting distances between lodgepole pine trees through mixed species plantations and overall reduction in use of lodgepole pine for regeneration in wet areas are the best strategies to reduce the spread of the disease and enhance future productivity of plantations in the study area.
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Barnes I, Wingfield MJ, Carbone I, Kirisits T, Wingfield BD. Population structure and diversity of an invasive pine needle pathogen reflects anthropogenic activity. Ecol Evol 2014; 4:3642-61. [PMID: 25478155 PMCID: PMC4224538 DOI: 10.1002/ece3.1200] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 07/02/2014] [Indexed: 11/09/2022] Open
Abstract
Dothistroma septosporum is a haploid fungal pathogen that causes a serious needle blight disease of pines, particularly as an invasive alien species on Pinus radiata in the Southern Hemisphere. During the course of the last two decades, the pathogen has also incited unexpected epidemics on native and non-native pine hosts in the Northern Hemisphere. Although the biology and ecology of the pathogen has been well documented, there is a distinct lack of knowledge regarding its movement or genetic diversity in many of the countries where it is found. In this study we determined the global population diversity and structure of 458 isolates of D. septosporum from 14 countries on six continents using microsatellite markers. Populations of the pathogen in the Northern Hemisphere, where pines are native, displayed high genetic diversities and included both mating types. Most of the populations from Europe showed evidence for random mating, little population differentiation and gene flow between countries. Populations in North America (USA) and Asia (Bhutan) were genetically distinct but migration between these continents and Europe was evident. In the Southern Hemisphere, the population structure and diversity of D. septosporum reflected the anthropogenic history of the introduction and establishment of plantation forestry, particularly with Pinus radiata. Three introductory lineages in the Southern Hemisphere were observed. Countries in Africa, that have had the longest history of pine introductions, displayed the greatest diversity in the pathogen population, indicating multiple introductions. More recent introductions have occurred separately in South America and Australasia where the pathogen population is currently reproducing clonally due to the presence of only one mating type.
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Affiliation(s)
- Irene Barnes
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria Pretoria, 0002, South Africa
| | - Michael J Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria Pretoria, 0002, South Africa
| | - Ignazio Carbone
- Department of Plant Pathology, Center for Integrated Fungal Research, North Carolina State University Raleigh, North Carolina, 27695
| | - Thomas Kirisits
- Department of Forest and Soil Sciences (DFS), Institute of Forest Entomology, Forest Pathology and Forest Protection (IFFF), University of Natural Resources and Life Sciences, Vienna (BOKU) Vienna, Austria
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria Pretoria, 0002, South Africa
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Bradshaw RE, Slot JC, Moore GG, Chettri P, de Wit PJGM, Ehrlich KC, Ganley ARD, Olson MA, Rokas A, Carbone I, Cox MP. Fragmentation of an aflatoxin-like gene cluster in a forest pathogen. THE NEW PHYTOLOGIST 2013; 198:525-535. [PMID: 23448391 DOI: 10.1111/nph.12161] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 12/25/2012] [Indexed: 06/01/2023]
Abstract
Plant pathogens use a complex arsenal of weapons, such as toxic secondary metabolites, to invade and destroy their hosts. Knowledge of how secondary metabolite pathways evolved is central to understanding the evolution of host specificity. The secondary metabolite dothistromin is structurally similar to aflatoxins and is produced by the fungal pine pathogen Dothistroma septosporum. Our study focused on dothistromin genes, which are widely dispersed across one chromosome, to determine whether this unusual distributed arrangement evolved from an ancestral cluster. We combined comparative genomics and population genetics approaches to elucidate the origins of the dispersed arrangement of dothistromin genes over a broad evolutionary time-scale at the phylum, class and species levels. Orthologs of dothistromin genes were found in two major classes of fungi. Their organization is consistent with clustering of core pathway genes in a common ancestor, but with intermediate cluster fragmentation states in the Dothideomycetes fungi. Recombination hotspots in a D. septosporum population matched sites of gene acquisition and cluster fragmentation at higher evolutionary levels. The results suggest that fragmentation of a larger ancestral cluster gave rise to the arrangement seen in D. septosporum. We propose that cluster fragmentation may facilitate metabolic retooling and subsequent host adaptation of plant pathogens.
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Affiliation(s)
- Rosie E Bradshaw
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Jason C Slot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Geromy G Moore
- Southern Regional Research Center, Agricultural Research Service, USDA, New Orleans, LA, 70124, USA
| | - Pranav Chettri
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Pierre J G M de Wit
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - Kenneth C Ehrlich
- Southern Regional Research Center, Agricultural Research Service, USDA, New Orleans, LA, 70124, USA
| | - Austen R D Ganley
- Institute of Natural Sciences, Massey University, Albany, New Zealand
| | - Malin A Olson
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Ignazio Carbone
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695-7244, USA
| | - Murray P Cox
- Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Scientific Opinion on the risk to plant health posed by Dothistroma septosporum (Dorog.) M. Morelet (Mycosphaerella pini E. Rostrup, syn. Scirrhia pini) and Dothistroma pini Hulbary to the EU territory with the identification and evaluation of risk reduct. EFSA J 2013. [DOI: 10.2903/j.efsa.2013.3026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry. PLoS Genet 2012; 8:e1003088. [PMID: 23209441 PMCID: PMC3510045 DOI: 10.1371/journal.pgen.1003088] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 09/19/2012] [Indexed: 01/07/2023] Open
Abstract
We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum (Cfu) (syn. Passalora fulva) and Dothistroma septosporum (Dse) that are closely related phylogenetically, but have different lifestyles and hosts. Although both fungi grow extracellularly in close contact with host mesophyll cells, Cfu is a biotroph infecting tomato, while Dse is a hemibiotroph infecting pine. The genomes of these fungi have a similar set of genes (70% of gene content in both genomes are homologs), but differ significantly in size (Cfu >61.1-Mb; Dse 31.2-Mb), which is mainly due to the difference in repeat content (47.2% in Cfu versus 3.2% in Dse). Recent adaptation to different lifestyles and hosts is suggested by diverged sets of genes. Cfu contains an α-tomatinase gene that we predict might be required for detoxification of tomatine, while this gene is absent in Dse. Many genes encoding secreted proteins are unique to each species and the repeat-rich areas in Cfu are enriched for these species-specific genes. In contrast, conserved genes suggest common host ancestry. Homologs of Cfu effector genes, including Ecp2 and Avr4, are present in Dse and induce a Cf-Ecp2- and Cf-4-mediated hypersensitive response, respectively. Strikingly, genes involved in production of the toxin dothistromin, a likely virulence factor for Dse, are conserved in Cfu, but their expression differs markedly with essentially no expression by Cfu in planta. Likewise, Cfu has a carbohydrate-degrading enzyme catalog that is more similar to that of necrotrophs or hemibiotrophs and a larger pectinolytic gene arsenal than Dse, but many of these genes are not expressed in planta or are pseudogenized. Overall, comparison of their genomes suggests that these closely related plant pathogens had a common ancestral host but since adapted to different hosts and lifestyles by a combination of differentiated gene content, pseudogenization, and gene regulation.
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Dale AL, Lewis KJ, Murray BW. Sexual reproduction and gene flow in the pine pathogen Dothistroma septosporum in British Columbia. PHYTOPATHOLOGY 2011; 101:68-76. [PMID: 20795853 DOI: 10.1094/phyto-04-10-0121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Dothistroma septosporum has caused a serious needle blight epidemic in the lodgepole pine forests in northwest British Columbia over the past several years. Although ascocarps had been observed in British Columbia, nothing was known about the contribution of sexual reproduction, gene flow and long-distance dispersal to the epidemic. Amplified fragment length polymorphism and mating-type markers in 19 sites were used to generate population and reproductive data. Overall, evidence suggests a mixed mode of reproduction. Haplotypic diversity was high, with 79 unique and 56 shared haplotypes (possible clones) identified from 192 fungal isolates. Overall, mating-type segregation did not differ significantly from 1:1; however, random mating was rejected in most populations in the index of association and parsimony tree-length permutation analyses using the full data set and, when using clone-corrected data sets, more of the smaller populations showed random mating. Two of the smaller populations consistently showed random mating for both tests using both clone-corrected and noncorrected data. High gene flow is suggested by no differentiation between 14 of the 19 sites, several of which came from young plantations where the pathogen was not likely present prior to the current outbreak. The remaining five sites showed some level of divergence, possibly due to historic separation and endemic pathogen populations. Results indicate a high evolutionary potential and long-distance dispersal in this pathogen, important to consider in future forest management.
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Affiliation(s)
- A L Dale
- Natural Resources and Environmental Studies Institute, University of Northern British Columbia, 3333 University Way, Prince George, BC V2N 4Z9, Canada.
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Ioos R, Fabre B, Saurat C, Fourrier C, Frey P, Marçais B. Development, comparison, and validation of real-time and conventional PCR tools for the detection of the fungal pathogens causing brown spot and red band needle blights of pine. PHYTOPATHOLOGY 2010; 100:105-114. [PMID: 19968556 DOI: 10.1094/phyto-100-1-0105] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Dothistroma pini, D. septosporum, and Lecanosticta acicola are fungal pathogens that cause severe foliage diseases in conifers. All three pathogens are listed as quarantine organisms in numerous countries throughout the world and, thus, are subject to specific monitoring. Detection and identification of these pathogens still often relies on cumbersome and unsatisfactory methods that are based upon the morphological characterization of fungal fruiting bodies and conidia. In this study, we present the development of several new molecular tools that enable a rapid and specific in planta detection of each of these pathogens. Several DNA extraction procedures starting from infected needles were compared and four commercial DNA extraction kits provided DNA of satisfactory quality for amplification by polymerase chain reaction (PCR). In addition, we developed several sets of conventional PCR primers, dual-labeled probes (DLPs), and duplex-scorpion probes (DSPs), all of which targeted each pathogen. Their ability to detect the pathogens in a series of naturally infected needle samples was compared. The quadruplex DLP real-time assay proved to be more sensitive than the DSP assay and conventional PCR but the two real-time probe formats yielded identical results in the naturally infected samples. Both real-time assays proved to be significantly superior to the technique of humid chamber incubation, which often failed to produce spores for the accurate identification of the pathogens.
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Affiliation(s)
- Renaud Ioos
- Laboratorie National de la protection des Végétaux, Station de mycologie, IFR 110, Domaine de Pixérécourt, Malzéville, France.
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BARNES I, CORTINAS MN, WINGFIELD MJ, WINGFIELD BD. Microsatellite markers for the red band needle blight pathogen,Dothistroma septosporum. Mol Ecol Resour 2008; 8:1026-9. [DOI: 10.1111/j.1755-0998.2008.02142.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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